It's not clear to me what this level of packaging and integration achieves compared to mounting a (not integrated) E6xx BGA and a separate Altera or Xilinx FPGA BGA onto the main PCB, interconnected by PCIe x1 or perhaps even x4. Then you would get a broader choice of FPGAs -- and perhaps a simpler PCB escape for the two packages compared to one 1466 ball beast.

The advantages of this MCM as stated in the brief include:* reduced board footprint* lower component count* simplified inventory control / manufacturing* single-vendor support

True, but forgive me if I'm not over the moon. The dream of integrated FPGA fabric into a heterogeneous SoC (same die) includes a very low latency and possibly cache coherent interconect between the processor(s) and the FPGA. But here the FPGA is on the other side of a narrow PCIe link. It can't share the Atom SoC's memory hierarchy / DRAM channels very effectively. It is probably a very long latency round trip from x86 software control / registers and L1$ data, to some registers or function units in the FPGA, and back to the x86. So I think of this as more of a super-flexible Atom SoC platform than a dream reconfigurable computing platform.

Virtex-II Pro, Virtex-4, and Virtex-5 offered devices with 0, 1, or 2 PowerPC cores. Xilinx once showed die floorplans of Virtex-II Pros with 4 PowerPC cores but if I recall correctly they never shipped such devices.